void _sir_par_trans (double *pt, double *p, int *parindex)
{
int nbasis = *(get_pomp_userdata_int("nbasis"));
int k;
pt[parindex[0]] = exp(GAMMA);
pt[parindex[1]] = exp(MU);
pt[parindex[2]] = exp(IOTA);
for (k = 0; k < nbasis; k++)
pt[parindex[3]+k] = exp(BETA[k]);
pt[parindex[4]] = exp(BETA_SD);
pt[parindex[6]] = expit(RHO);
from_log_barycentric(pt+parindex[7],&S0,3);
}
///////////////////////////////////////////////////////////////////
// DEFINE THE MEASUREMENT MODEL
///////////////////////////////////////////////////////////////////
void null_chickenpox_meas_sim (double *y, double *x, double *p,
int *obsindex, int *stateindex, int *parindex, int *covindex,
int ncovar, double *covar, double t) {
double report_rate, tau;
// PUT PARS ON NATURAL SCALE
tau = exp(LOGTAU);
report_rate = expit(LOGITRHO);
CHICKENPOX = rnorm(report_rate*I,tau*I);
if (CHICKENPOX >= 0) {
CHICKENPOX = nearbyint(CHICKENPOX);
} else {CHICKENPOX = 0;}
}
///////////////////////////////////////////////////////////////////
// DEFINE THE MEASUREMENT DENSITY FOR CALCULATING THE LIKELIHOOD
///////////////////////////////////////////////////////////////////
void null_chickenpox_meas_dens (double *lik, double *y, double *x, double *p, int give_log,
int *obsindex, int *stateindex, int *parindex, int *covindex,
int ncovar, double *covar, double t) {
double report_rate, tau;
double tol = 1.0e-18;
// PUT PARS ON NATURAL SCALE
tau = exp(LOGTAU);
report_rate = expit(LOGITRHO);
if(CHICKENPOX > 0.0){
*lik = pnorm(CHICKENPOX+0.5,report_rate*I,tau*I,1,0) - pnorm(CHICKENPOX-0.5,report_rate*I,tau*I,1,0)+ tol;
} else{
*lik = pnorm(CHICKENPOX+0.5,report_rate*I,tau*I,1,0)+ tol;
}
if (give_log) *lik = log(*lik);
if (!isfinite(*lik)) Rprintf("chickenpox_meas_dens %lg %lg %lg %lg %lg\n",CHICKENPOX,report_rate,tau,I,*lik);
}